Identification of submergence tolerance QTLs/genes during seed germination in 432 rice varieties by GWAS

Submergence stress is a major obstacle limiting the application of direct seeding in rice cultivation. Therefore, understanding the genetic basis of submergence tolerance in rice is of great significance for identifying favorable genes and developing superior rice varieties. However, few studies have focused on submergence tolerance during seed germination; thus, the genetic basis of submergence tolerance at this stage deserves more attention.

In this study, a natural population of 432 rice varieties collected from 25 provinces in China and other countries was used for the first time to evaluate submergence tolerance during seed germination. Population structure analysis revealed that this population was divided into two groups and was rich in genetic diversity. Our findings confirm that japonica rice is more tolerant to submergence than indica rice during seed germination. A genome-wide association study (GWAS) was performed using the phenotypic data of 432 rice varieties and a 3,548,101 single-nucleotide polymorphism (SNP) dataset using a mixed linear model. Thirteen QTLs (P < 0.0001) were identified for the coleoptile length (CL) under submergence (10 cm depth of water), of which four QTLs (qCL3-1, qCL4-2, qCL5-1, and qCL5-2) colocalized with those from previous studies, while nine QTLs (qCL2-1, qCL2-2, qCL2-3, qCL2-4, qCL3-2, qCL4-1, qCL8-1, qCL8-2, and qCL9) were reported for the first time. Among these QTLs, qCL9, which harbored the most significant SNP, explained most of the phenotypic variation. Using quantitative real-time polymerase chain reaction (qRT-PCR) analysis and phenotypic identification of the knockout lines, three genes (LOC_Os09g11590, LOC_Os09g11660, and LOC_Os09g11760) were identified as candidates for qCL9. There were 28, 13, and 13 non-synonymous SNPs in LOC_Os09g11590, LOC_Os09g11660, and LOC_Os09g11760, respectively, from which 5, 3, and 5 haplotypes were detected in rice varieties.

This natural population, consisting of 432 rice varieties combined with high-density SNPs, provides a valuable resource for identifying rice QTLs/genes in the future. The detected QTLs/genes associated with submergence tolerance during seed germination in rice offer new insights for gene discovery and will facilitate the breeding of rice varieties with improved tolerance to submergence stress.